Docking pose detail

Molecular metrics status: done

RDKit SASA-based burial metrics are cached.

SASA cached

T19

T. brucei TR (NADPH binding site) T. brucei NADPH binding site

Ligand Z57782579

PDB2WOV↗

3D complex viewer

Strict H-bonds Permissive H-bonds

Viewer legend

Protein receptor

Pocket residues

Cofactor context

Docked ligand

Overall assessment

Weak SASA cached

Weak or marginal quality

Binding strong Geometry medium Native mixed SASA done

Strain ΔE

37.4 kcal/mol

Protein clashes

Internal clashes

Native overlap

contact recall 0.33, Jaccard 0.23, H-bond role recall 0.40

Burial

94%

Hydrophobic fit

90%

Reason: no major geometry red flags detected

2 protein-contact clashes

Molecular report

Full metrics ↗

Weak Marginal quality. Consider only alongside better-scoring alternatives.

✓ Excellent LE (-1.131 kcal/mol/HA) ✓ Good fit quality (FQ -11.01) ✓ Deep burial (94% SASA buried) ✓ Lipophilic contacts well-matched (90%) ✗ Very high strain energy (37.4 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (15)

Score

-35.047

kcal/mol

-1.131

kcal/mol/HA

Fit Quality

-11.01

FQ (Leeson)

HAC

heavy atoms

421

LogP

1.80

cLogP

Final rank

3.5582

rank score

Inter norm

-1.108

normalised

Contacts

H-bonds 5

Strain ΔE

37.4 kcal/mol

SASA buried

94%

Lipo contact

90% BSA apolar/total

SASA unbound

694 Å²

Apolar buried

586 Å²

Interaction summary

HBA 2 PC 1 HY 9 PI 1 CLASH 2

HBD/HBA · H-bonds (geometric)

HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 2.

PC · Polar contacts (possible, no H geometry)

HBD?/HBA? — heavy-atom distance only, H geometry unavailable. May be real H-bonds.

PI · π–π interactions

Native π–π recall is disabled because no explicit native π–π reference was stored.

HY · Hydrophobic contacts

CLASH · Clashes

Native ligand reference

★ reference

Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.

Name	2WOV	Contacts	27
Pose	Open native pose	HB	0
IFP residues	ALA284 ALA365 ARG222 ARG228 ARG287 ASN223 ASN254 GLN165 GLU202 GLY195 GLY196 GLY197 GLY286 ILE199 ILE285 LEU227 LEU334 LYS60 MET333 NDP800 PHE198 PHE367 PRO167 SER200 TYR221 VAL194 VAL366
Current overlap	9	Native recall	0.33
Jaccard	0.23	RMSD	-
HB strict	2	Strict recall	0.17
HB same residue+role	2	HB role recall	0.40
HB same residue	2	HB residue recall	0.50

Protein summary

493 residues

Protein target	T19	Atoms	7541
Residues	493	Chains	1
Residue summary	VAL:768; LYS:704; LEU:703; ILE:532; GLU:450; THR:434; ARG:408; PHE:400; ALA:390; ASN:350; PRO:350; GLY:336; SER:330; TYR:294; ASP:264; MET:221

Receptor context

1 kept / 0 excluded

Receptor context filtering: interactions and SASA are computed against protein atoms plus allowed cofactors/ions. Native ligand-like HETATM partners are excluded from scoring.

Kept context 1 Excluded HETATM 0

Kept cofactors / ions

C:NDP800

All stored poses for this docking hit

Pose	Final rank	Inter norm	Score	HB	CT	CT overlap	CT recall	HB role rec.	RMSD	Excluded
539	3.5582245506612225	-1.10848	-35.0473	5	22	9	0.33	0.40	-	no	Current

Molecular metrics

RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.

✓ Metrics available

Scoring & efficiency

Docking score -35.047kcal/mol

Ligand efficiency (LE) -1.1306kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -11.014

LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe

Heavy atom count 31HA

Physicochemical properties

Molecular weight 420.5Da

Lipinski: ≤ 500 Da

LogP (cLogP) 1.80

Lipinski: ≤ 5

Rotatable bonds 3

Conformational strain (MMFF94s)

Strain energy (ΔE) 37.35kcal/mol

< 5 good · 5–10 marginal · > 10 problematic

Docked FF energy -66.79kcal/mol

Minimised FF energy -104.14kcal/mol

SASA & burial

✓ computed

SASA (unbound) 693.7Å²

Total solvent-accessible surface area of free ligand

BSA total 651.9Å²

Buried surface area upon binding

BSA apolar 586.0Å²

Hydrophobic contacts buried

BSA polar 65.9Å²

Polar contacts buried

Fraction buried 94.0%

> 60 % indicates good pocket engagement

Lipophilic contact ratio 89.9%

BSA apolar / BSA total — high = hydrophobic driver

Δ Non-polar SASA -3230.8Å²

SASA_nonpolar(complex) − SASA_nonpolar(receptor) − SASA_nonpolar(ligand free). Negative = non-polar surface buried upon binding. Requires full polarity-decomposed SASA computation.

Receptor non-polar SASA 4064.7Å²

Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)

Complex non-polar SASA 1461.7Å²

Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)